Hi Msev, if you download the latest version you'll find what you're looking for. On the "Score/Rank"-page you can export docking scores and also docking poses in pdb format. If you save a list containing different ligands it might indeed look weired when you reload the file into pymol since pymol makes the bonds only based on the first model. But you can convert the poses.pdb to a mol2 file with babel and load that into pymol. That should look nice.
Cheers, Daniel On Monday 15 February 2010 08:05:35 pm Marko S wrote: > Hello, > > I'm quite a novice user of PyMOL but I am already impressed at the speed > and beauty of the rendering. But I have some questions regarding it's use > for viewing results of Autodock. > So I normally proceed as follows, i open the PDB molecule say fetch BLABLA > and i get the pdb file...Then i have two options, one is to simply open the > .dlg file then i get only one ligand results which i scrool with the play > button to see all the results, but there is also an option (i use the > autodock plugin, and with that i get all of the results on the screen), but > the problem is how to save everything together in one pdb. file. I tried > with the "write complex.pdb" but it made a strange mess when i look with > other pdb viewers such as Viewerlite. > What can you suggest me to do? > > Thank you for the answers! > > Msev > -- Dr. Daniel Seeliger Computational Biomolecular Dynamics Group Max-Planck-Institute for Biophysical Chemistry Tel. +49 (0) 551-201-2310 http://wwwuser.gwdg.de/~dseelig ------------------------------------------------------------------------------ SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
